There evidence that in many ecosystems more than 99% of the microbial population resists laboratory cultivation. N. R. Pace, “A Molecular View of Microbial Diversity and the Biosphere”, Science 276, 734 (1997). This has led to the suggestion that microbial ecosystems in human beings are more complex than previously suspected, and that some or many of the uncultivatable microbes may be infectious agents. D. A. Relman, “The Search for Unrecognized Pathogens”, Science 284, 1308 (1999).
A substantial number of illnesses resemble infectious disease, and unexplained death or critical illnesses occur in 0.5 persons per 100,000 population. B. A. Perkins et al., “Unexplained Deaths Due to Possibly Infectious Causes in the United States: Defining the Problem and Designing Surveillance and Laboratory Approaches”, Emerging Inject. Dis. 2, 47 (1996). Many such pathogens resist identification by traditional phenotypic methods, which has led to the development of genotypic methods of pathogen identification.
As a result, the last twenty years have seen a growing list of connections between human disease and previously unsuspected microbial pathogens. TABLE 1 lists examples of human disease and associated microbial pathogens revealed during the past 20 years. All of these infectious agents, except Heliobacter pylori, were first identified directly from clinical specimens using genotypic approaches.
TABLE 1DiseaseInfectious AgentPeptic ulcer diseaseHeliobacter pyloriNon-A, non-B hepatitisHepatitis C virusBacillary angiomatosisBartonella henselaeWhipple's diseaseTropheryma whippeliiHantavirus pulmonary syndromeSin Nombre virusKaposi's sarcomaKaposi's sarcoma-associatedherpesvirus
Although the human body offers a highly diverse ecosystem for bacteria and viruses, it has been difficult to make precise measurements of diversity and population distribution because many organisms living within it have proven difficult or impossible to culture.
Accordingly, there is a need in the art for techniques and apparatuses for characterizing and analyzing bacteria and viruses existing in a variety of environments.